# Generated by roxygen2: do not edit by hand export("colTree<-") export("colTreeNames<-") export("referenceSeq<-") export("rowTree<-") export("rowTreeNames<-") export(LinkDataFrame) export(TreeSummarizedExperiment) export(addLabel) export(aggTSE) export(aggValue) export(asLeaf) export(asPhylo) export(changeTree) export(colLinks) export(colTree) export(colTreeNames) export(convertNode) export(countLeaf) export(countNode) export(detectLoop) export(distNode) export(findAncestor) export(findChild) export(findDescendant) export(findOS) export(findSibling) export(isLeaf) export(joinNode) export(makeTSE) export(matTree) export(printNode) export(referenceSeq) export(resolveLoop) export(rowLinks) export(rowTree) export(rowTreeNames) export(shareNode) export(showNode) export(signalNode) export(subsetByLeaf) export(subsetByNode) export(toTree) export(trackNode) export(transNode) export(unionLeaf) exportClasses(LinkDataFrame) exportClasses(TreeSummarizedExperiment) exportMethods("[") exportMethods("[<-") exportMethods("colTree<-") exportMethods("colTreeNames<-") exportMethods("colnames<-") exportMethods("referenceSeq<-") exportMethods("rowTree<-") exportMethods("rowTreeNames<-") exportMethods("rownames<-") exportMethods(cbind) exportMethods(colLinks) exportMethods(colTree) exportMethods(colTreeNames) exportMethods(rbind) exportMethods(referenceSeq) exportMethods(rowLinks) exportMethods(rowTree) exportMethods(rowTreeNames) exportMethods(subsetByLeaf) exportMethods(subsetByNode) exportMethods(updateObject) exportMethods(vertical_slot_names) import(S4Vectors) import(SingleCellExperiment) import(methods) importClassesFrom(S4Vectors,DataFrame) importClassesFrom(SingleCellExperiment,SingleCellExperiment) importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment) importClassesFrom(SummarizedExperiment,SummarizedExperiment) importFrom(BiocParallel,bplapply) importFrom(Biostrings,DNAStringSet) importFrom(Biostrings,DNAStringSetList) importFrom(IRanges,relist) importFrom(S4Vectors,DataFrame) importFrom(S4Vectors,head) importFrom(S4Vectors,metadata) importFrom(S4Vectors,tail) importFrom(SummarizedExperiment,"colData<-") importFrom(SummarizedExperiment,"rowData<-") importFrom(SummarizedExperiment,assays) importFrom(ape,keep.tip) importFrom(ape,reorder.phylo) importFrom(ape,rtree) importFrom(dplyr,'%>%') importFrom(dplyr,arrange_all) importFrom(dplyr,group_by) importFrom(dplyr,mutate) importFrom(dplyr,mutate_if) importFrom(dplyr,row_number) importFrom(methods,as) importFrom(methods,callNextMethod) importFrom(methods,is) importFrom(methods,new) importFrom(methods,setClass) importFrom(methods,setOldClass) importFrom(rlang,.data) importFrom(stats,reorder) importFrom(stats,setNames) importFrom(treeio,as.phylo) importFrom(utils,flush.console) importMethodsFrom(SingleCellExperiment,show) importMethodsFrom(SummarizedExperiment,rbind)